Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Efficient workflow for the investigation of the catalytic cycle of water oxidation catalysts: Combining GFN-xTB and density functional theory.

ABSTRACT: Photocatalytic water oxidation remains the bottleneck in many artificial photosynthesis devices. The efficiency of this challenging process is inherently linked to the thermodynamic and electronic properties of the chromophore and the water oxidation catalyst (WOC). Computational investigations can facilitate the search for favorable chromophore-catalyst combinations. However, this remains a demanding task due to the requirements on the computational method that should be able to correctly describe different spin and oxidation states of the transition metal, the influence of solvation and the different rates of the charge transfer and water oxidation processes. To determine a suitable method with favorable cost/accuracy ratios, the full catalytic cycle of a molecular ruthenium based WOC is investigated using different computational methods, including density functional theory (DFT) with different functionals (GGA, Hybrid, Double Hybrid) as well as the semi-empirical tight binding approach GFN-xTB. A workflow with low computational cost is proposed that combines GFN-xTB and DFT and provides reliable results. GFN-xTB geometries and frequencies combined with single-point DFT energies give free energy changes along the catalytic cycle that closely follow the full DFT results and show satisfactory agreement with experiment, while significantly decreasing the computational cost. This workflow allows for cost efficient determination of energetic, thermodynamic and dynamic properties of WOCs.

SUBMITTER: Menzel JP

PROVIDER: S-EPMC8456855 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Ferrate(VI) Oxidation Mechanism of Substituted Anilines: A Density Functional Theory Investigation.

Project description:Ferrate(VI) (Fe(VI)) is a promising oxidant coagulant and disinfectant for the degradation of organic micropollutants. However, it is hard to elucidate the detailed oxidation mechanism through the current experimental approaches. Substituted anilines (SANs) are important chemical compounds that are widely used in many industries. This paper presents the use of density functional theory (DFT) to understand the oxidation mechanism of SANs by Fe(VI) and the effect of substituents. The calculation results revealed that the primary oxidations of SANs follow the hydrogen atom transfer (HAT) mechanism. Interestingly, the hydroxyl oxygen of HFeO4 - is more reactive than the carbonyl oxygen when reacting with SANs. The formation of the SAN radical is crucial, and all of the products are formed from it. Azobenzene is more favorable to generate the above products. In addition, the obtained results indicate that this kind of substituent has a much greater influence on the reaction rather than the position. Thus, the present study provides a valuable insight into the transformation pathways of SANs in the Fe(VI) oxidation process and the effects of the substituent on oxidation. These results will advance the understanding of Fe(VI) involved in wastewater treatment.

| S-EPMC8190916 | biostudies-literature

Revealing the structure of a catalytic combustion active-site ensemble combining uniform nanocrystal catalysts and theory insights.

Project description:Supported metal catalysts are extensively used in industrial and environmental applications. To improve their performance, it is crucial to identify the most active sites. This identification is, however, made challenging by the presence of a large number of potential surface structures that complicate such an assignment. Often, the active site is formed by an ensemble of atoms, thus introducing further complications in its identification. Being able to produce uniform structures and identify the ones that are responsible for the catalyst performance is a crucial goal. In this work, we utilize a combination of uniform Pd/Pt nanocrystal catalysts and theory to reveal the catalytic active-site ensemble in highly active propene combustion materials. Using colloidal chemistry to exquisitely control nanoparticle size, we find that intrinsic rates for propene combustion in the presence of water increase monotonically with particle size on Pt-rich catalysts, suggesting that the reaction is structure dependent. We also reveal that water has a near-zero or mildly positive reaction rate order over Pd/Pt catalysts. Theory insights allow us to determine that the interaction of water with extended terraces present in large particles leads to the formation of step sites on metallic surfaces. These specific step-edge sites are responsible for the efficient combustion of propene at low temperature. This work reveals an elusive geometric ensemble, thus clearly identifying the active site in alkene combustion catalysts. These insights demonstrate how the combination of uniform catalysts and theory can provide a much deeper understanding of active-site geometry for many applications.

| S-EPMC7334474 | biostudies-literature

Density Functional Theory Investigation of the NiO@Graphene Composite as a Urea Oxidation Catalyst in the Alkaline Electrolyte.

Project description:Developing efficient and low-cost urea oxidation reaction (UOR) catalysts is a promising but still challenging task for environment and energy conversion technologies such as wastewater remediation and urea electrolysis. In this work, NiO nanoparticles that incorporated graphene as the NiO@Graphene composite were constructed to study the UOR process in terms of density functional theory. The single-atom model, which differed from the previous heterojunction model, was employed for the adsorption/desorption of urea and CO2 in the alkaline media. As demonstrated from the calculated results, NiO@Graphene prefers to adsorb the hydroxyl group than urea in the initial stage due to the stronger adsorption energy of the hydroxyl group. After NiOOH@Graphene was formed in the alkaline electrolyte, it presents excellent desorption energy of CO2 in the rate-determining step. Electronic density difference and the d band center diagram further confirmed that the Ni(III) species is the most favorable site for urea oxidation while facilitating charge transfer between urea and NiO@Graphene. Moreover, graphene provides a large surface for the incorporation of NiO nanoparticles, enhancing the electron transfer between NiOOH and graphene and promoting the mass transport in the alkaline electrolyte. Notably, this work provides theoretical guidance for the electrochemical urea oxidation work.

| S-EPMC8260271 | biostudies-literature

Mechanistic investigations on Pinnick oxidation: a density functional theory study.

Project description:A computational study on Pinnick oxidation of aldehydes into carboxylic acids using density functional theory (DFT) calculations has been evaluated with the (SMD)-M06-2X/aug-pVDZ level of theory, leading to an important understanding of the reaction mechanism that agrees with the experimental observations and explaining the substantial role of acid in driving the reaction. The DFT results elucidated that the first reaction step (FRS) proceeds in a manner where chlorous acid reacts with the aldehyde group through a distorted six-membered ring transition state to give a hydroxyallyl chlorite intermediate that undergoes a pericyclic fragmentation to release the carboxylic acid as a second reaction step (SRS). 1H NMR experiments and simulations showed that hydrogen bonding between carbonyl and t-butanol is unlikely to occur. Additionally, it was found that the FRS is a rate-determining and thermoneutral step, whereas SRS is highly exergonic with a low energetic barrier due to the Cl(III) → Cl(II) reduction. Frontier molecular orbital analysis, intrinsic reaction coordinate, molecular dynamics and distortion/interaction analysis further supported the proposed mechanism.

| S-EPMC7062072 | biostudies-literature

Thermodynamic Properties of Hydrogen-Producing Cobaloxime Catalysts: A Density Functional Theory Analysis.

Project description:Density functional theory calculations were carried out to study the electrochemical properties including reduction potentials, pK a values, and thermodynamic hydricities of three prototypical cobaloxime complexes, Co(dmgBF2)2 (dmgBF2 = difluoroboryl-dimethylglyoxime), Co(dmgH)2 (dmgH = dimethylglyoxime), and Co(dmgH)2(py)(Cl) (py = pyridine) in the acetonitrile (AN)-water solvent mixture. The electrochemical properties of Co(dmgBF2)2 in pure AN and pure water were also considered for comparison to reveal the key roles of the solvent on the catalytic reaction. In agreement with previous studies, hydrogen production pathways starting from reduction of the resting state of CoII and involving formation of the CoIIIH and CoIIH intermediates are the favorable ones for both bimetallic and monometallic pathways. However, we found that in pure AN, both the CoIIIH and CoIIH intermediates can react with a proton to produce H2. In the presence of water in the solvent, the reduction of CoIIIH to CoIIH is necessary for the reaction with a proton to occur to form H2. This suggests that it is possible to design catalytic systems by suitably tuning the composition of the AN-water mixture. We also identified the key role of axial coordination of the solvent molecules in affecting the catalytic reaction, which allows further catalyst design strategy. The highest hydride donor ability of Co(dmgH)2(py)(Cl) indicates that this complex displays the best catalytic hydrogen-producing performance among the three cobaloximes studied in this work.

| S-EPMC6649079 | biostudies-literature

Selective Oxidation of HMF via Catalytic and Photocatalytic Processes Using Metal-Supported Catalysts.

Project description:In this study, 5-hydroxymethylfurfural (HMF) oxidation was carried out via both the catalytic and the photocatalytic approach. Special attention was devoted to the preparation of the TiO₂-based catalysts, since this oxide has been widely used for catalytic and photocatalytic application in alcohol oxidation reactions. Thus, in the catalytic process, the colloidal heterocoagulation of very stable sols, followed by the spray-freeze-drying (SFD) approach, was successfully applied for the preparation of nanostructured porous TiO₂-SiO₂ mixed-oxides with high surface areas. The versatility of the process made it possible to encapsulate Pt particles and use this material in the liquid-phase oxidation of HMF. The photocatalytic activity of a commercial titania and a homemade oxide prepared with the microemulsion technique was then compared. The influence of gold, base addition, and oxygen content on product distribution in the photocatalytic process was evaluated.

| S-EPMC6278393 | biostudies-literature

Dataset on density functional theory investigation of ternary Heusler alloys.

Project description:This paper contains data and results from Density Functional Theory (DFT) investigation of 423 distinct X2YZ ternary full Heusler alloys, where X and Y represent elements from the D-block of the periodic table and Z signifies element from main group. The study encompasses both "regular" and "inverse" Heusler phases of these alloys for a total of 846 potential materials. For each specific alloy and each phase, a range of information is provided including total energy, formation energy, lattice constant, total and site-specific magnetic moments, spin polarization as well as total and projected density of electronic states. The aim of creating this dataset is to provide fundamental theoretical insights into ternary X2YZ Heusler alloys for further theoretical and experimental analysis.

| S-EPMC10788214 | biostudies-literature

Density Functional Theory Investigation of As(III) S-Adenosylmethionine Methyltransferase.

Project description:Arsenic is one of the most pervasive environmental toxins. It enters our water and food supply through many different routes, including the burning of fossil fuels, the application of arsenic-based herbicides, and natural sources. Using a density functional theory (DFT) cluster approach, the mechanism of arsenic (III) S-adenosylmethionine methyltransferases and various selenium-containing analogues was investigated. Notably, the methylation of arsenic by arsenic (III) S-adenosylmethionine is proposed to be a way to remove arsenic from contaminated water or soil. From the DFT cluster results, it was found that the selective substitution of the active-site Cys44, Cys72, and Cys174 residues with selenocysteines had a marginal effect on the barrier for CH3 transfer. Specifically, the average Gibbs activation energy was calculated to be only 4.2 kJ mol-1 lower than the Gibbs activation energy of 107.4 kJ mol-1 for the WT enzyme. However, importantly, it was found that with selective mutation, the methylation process becomes considerably more exergonic, where the methylation reaction can be made to be 26.4 kJ mol-1 more exergonic than the reaction catalyzed by the WT enzyme. Therefore, we propose that the selective substitution of the active-site Cys44, Cys72 and Cys174 residues with selenocysteines could make the process of methylation and volatilization more advantageous for bioremediation.

| S-EPMC7450623 | biostudies-literature

Oxidation of Electron-Deficient Phenols Mediated by Hypervalent Iodine(V) Reagents: Fundamental Mechanistic Features Revealed by a Density Functional Theory-Based Investigation.

Project description:Hypervalent iodine (HVI) compounds are efficient reagents for the double oxidative dearomatization of electron-rich phenols to o-quinones. We recently reported that an underexplored class of iodine(V) reagents possessing bidentate bipyridine ligands, termed Bi(N)-HVIs, could dearomatize electron-poor phenols for the first time. To understand the fundamental mechanistic basis of this unique reactivity, density functional theory (DFT) was utilized. In this way, different pathways were explored to determine why Bi(N)-HVIs are capable of facilitating these challenging transformations while more traditional hypervalent species, such as 2-iodoxybenzoic acid (IBX), cannot. Our calculations reveal that the first redox process is the rate-determining step, the barrier of which hinges on the identity of the ligands bound to the iodine(V) center. This crucial process is composed of three steps: (a) ligand exchange, (b) hypervalent twist, and (c) reductive elimination. We found that strong coordinating ligands disfavor these elementary steps, and, for this reason, HVIs bearing such ligands cannot oxidize the electron-poor phenols. In contrast, the weakly coordinating triflate ligands in Bi(N)-HVIs allow for the kinetically favorable oxidation. It was identified that trapping in situ-generated triflic acid is a key role played by the bidentate bipyridine ligands in Bi(N)-HVIs as this serves to minimize the decomposition of the ortho-quinone product.

| S-EPMC9389628 | biostudies-literature

A nonenzymatic acid/peracid catalytic cycle for the Baeyer-Villiger oxidation.

Project description:The combined action of carbodiimide and hydrogen peroxide upon exposure to carboxylic acid catalysts serves to generate transient peracids that can be engaged in the Baeyer-Villiger rearrangement of ketones to lactones. Up to 35 turnovers of the catalytic cycle may be achieved. The conditions are especially useful in the context of reactive cyclohexanones, and allow the use of H2O2 as the terminal oxidant. A singular example of a chiral catalyst demonstrates, in principle, that enantioselective catalysis will be possible with this strategy for catalyst turnover.

| S-EPMC4125978 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data